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Glycolytic and gluconeogenic pathway in B. phymatum. EC 1.1.1.44, 6-phosphogluconate dehydrogenase; EC 1.2.1.12, glyceraldehyde-3-phosphate dehydrogenase; EC 2.7.1.2, glucokinase; EC 2.7.1.4, fructokinase; EC 2.7.1.11, 6- phosphofructokinase; EC 2.7.1.12, gluconokinase; EC 2.7.1.40, pyruvate kinase; EC 2.7.2.3, phosphoglycerate kinase; EC 3.1.3.11, FBPase; EC 4.1.2.13, fructose 1,6-bisphosphate aldolase; EC 4.1.2.14, 2-dehydro-3-deoxyphosphogluconate aldolase; EC 4.2.1.11, enolase; EC 4.2.1.12, phosphogluconate dehydratase; EC 5.3.1.9, glucose-6-phosphate isomerase; EC 5.4.2.1, phosphoglycerate mutase.
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Burkholderia phymatum STM815 is a β-rhizobial strain that can effectively nodulate several species of the large legume genus Mimosa. Two Tn5-induced mutants of this strain, KM16-22 and KM51, failed to form root nodules on Mimosa pudica, but still caused root hair deformation, which is one of the early steps of rhizobial infection. Both mutants grew...
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... pathways for carbon metabolism outlined in Fig. 1 are based primarily on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for B. phymatum. Phosphoglycerate mutase (PGM) is known to be an important enzyme for both glycolysis and gluconeogenesis (Fothergill-Gilmore & Watson, 1989). It catalyses the reversible isomerization of 2-phosphoglycerate (2-PGA) and ...
Citations
... The enzyme phosphoglycerate mutase (PGAM) is responsible for the conversion of 3-phosphoglycerate to 2-phosphoglycerate (Chen et al., 2012). In the present investigation, it was observed that the expression of the PGAM gene was significantly increased in response to exposure to cadmium. ...
Cadmium is a persistent heavy metal commonly found in aquatic ecosystems and has a strong toxic effect on organisms. The sensitivity of phytoplankton to environmental changes and its role as an indicator of aquatic ecosystem health have been well-established. However, the mechanisms by which phytoplankton respond to cadmium remain incompletely understood. In this study, we chose the typical planktonic diatom Cyclotella meneghiniana Kützing, by integrating physiological-biochemical data and transcriptome analysis, to reveal the molecular mechanisms of C. meneghiniana responing to cadmium. Under cadmium stress, the cell density and chlorophyll-a content of C. meneghiniana significantly decreased, while MDA content and SOD activity gradually increased. At 72 h of cadmium stress, we found that at this time point, cell abundance and physiological variation were very significant, therefore we selected 72 h for subsequent analysis. To better understand the cadmium stress response mechanisms of C. meneghiniana, a de novo transcriptome method was used to analyse C. meneghiniana under cadmium stress for 72 h, and 1704 (M vs. CK) and 4788 (H vs. CK) differentially expressed genes were found. Our results showed that the changes in gene expression were closely correlated to the physiological-biochemical changes. Although cadmium stress could promote the nitrogen metabolism pathway, ROS scavenging system, and photosynthesis. While, C. meneghiniana under medium and high concentrations of cadmium can also limit various intracellular metabolic pathways, such as the MAPK pathway and phosphati-dylinositol metabolic pathway, and the degree of inhibition increases with the increase of stress concentration. In present study, the complete molecular mechanism of the planktonic diatom response to cadmium has been established, which provided important information for further studies on heavy metal pollutants and the multiple functional genes responsible for cadmium sensitivity and tolerance in planktonic diatoms.
... Among the LA PGPB strains, Pseudomonas strains exhibited a higher abundance of CAZymes than did K1, K2, and K3 PGPB strains, indicating that this genus could be developed into an ideal interfoliar biocontrol agent (43). Conversely, among the SA PGPB strains, Burkholderia strains possessed a higher concentration of genes encoding carbohydrate metabolism enzymes, suggesting that they have diverse mechanisms for carbohydrate utilization (44). ...
Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.
... It would appear as if certain rhizobial enzymes involved in carbon metabolism play an important role during symbiosis. Mutants of P. phymatum for phosphoglycerate mutase (Bphy_0266), an enzyme important for glycolysis and gluconeogenesis, and fructose 1,6biphosphatase (Bphy_0685), a regulatory enzyme in gluconeogenesis, are not able to induce ITs or nodules, although they still possess the ability to cause root hair deformation [187]. Some of the possible explanations for this observation are that either the accumulation of intermediates would interfere during nodulation, or that growth by gluconeogenesis is indispensable for P. phymatum during the early steps of nodulation [187]. ...
... Mutants of P. phymatum for phosphoglycerate mutase (Bphy_0266), an enzyme important for glycolysis and gluconeogenesis, and fructose 1,6biphosphatase (Bphy_0685), a regulatory enzyme in gluconeogenesis, are not able to induce ITs or nodules, although they still possess the ability to cause root hair deformation [187]. Some of the possible explanations for this observation are that either the accumulation of intermediates would interfere during nodulation, or that growth by gluconeogenesis is indispensable for P. phymatum during the early steps of nodulation [187]. ...
A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.
... Mice infected with a mutant strain of Staphylococcus aureus lacking iPGM exhibited milder disease symptoms (Radin et al., 2019). Moreover, the dPGM of Burkholderia phymatum plays a crucial role in the formation of root nodules in Mimosa pudica (Chen et al., 2012). However, the functions of PGMs in Ac are yet to be elucidated. ...
... Compared with Ac(EV) and bdpmAc:Tn (BdpmAc), our findings also demonstrated that bdpmAc:Tn(EV) did not grow well in M9 medium with glucose or fructose, which are precursors in the glycolysis pathway. In agreement with our observations, a dPGM knockout mutant in Burkholderia phymatum also showed similar growth patterns in a previous study (Chen et al., 2012). Interestingly, bdpmAc:Tn(EV) did not grow in M9 with fructose but exhibited moderate to low growth rates in M9 supplemented with glucose. ...
... All experiments showed similar patterns. media (Chen et al., 2012). In agreement with this observation, the growth rates of bdpmAc:Tn(EV) were comparable to those of Ac(EV) and bdpmAc:Tn(BdpmAc). ...
Acidovorax citrulli ( Ac ) is a gram-negative bacterium that causes bacterial fruit blotch (BFB) disease in cucurbit crops including watermelon. However, despite the great economic losses caused by this disease worldwide, Ac -resistant watermelon cultivars have not been developed. Therefore, characterizing the virulence factors/mechanisms of Ac would enable the development of effective control strategies against BFB disease. The 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (BdpM) is known to participate in the glycolysis and gluconeogenesis pathways. However, the roles of the protein have not been characterized in Ac . To elucidate the functions of BdpmAc (Bdpm in Ac ), comparative proteomic analysis and diverse phenotypic assays were conducted using a bdpmAc knockout mutant ( bdpmAc:Tn ) and a wild-type strain. The virulence of the mutant to watermelon was remarkably reduced in both germinated seed inoculation and leaf infiltration assays. Moreover, the mutant could not grow with fructose or pyruvate as a sole carbon source. However, the growth of the mutant was restored to levels similar to those of the wild-type strain in the presence of both fructose and pyruvate. Comparative proteomic analyses revealed that diverse proteins involved in motility and wall/membrane/envelop biogenesis were differentially abundant. Furthermore, the mutant exhibited decreased biofilm formation and twitching halo size. Interestingly, the mutant exhibited a higher tolerance against osmotic stress. Overall, our findings suggest that BdpmAc affects the virulence, glycolysis/gluconeogenesis, biofilm formation, twitching halo size, and osmotic tolerance of Ac , suggesting that this protein has pleiotropic properties. Collectively, our findings provide fundamental insights into the functions of a previously uncharacterized phosphoglycerate mutase in Ac .
... Bean plants inoculated with these mutants showed a significantly reduced nitrogenase activity and a lower N content compared to plants infected with the wild type. In previous studies [82,83], three genes were shown to be important during symbiosis with M. pudica: Bphy_0456, involved in the biosynthesis of branched-chain amino acids, Bphy_0685, coding for a fructose 1,6-bisphosphatase, and Bphy_0266 (gpmA), coding for a phosphoglycerate mutase. The expression of these three genes was not regulated in bean root nodules compared to free-living conditions, suggesting that P. phymatum may upregulate a different set of genes in its natural host plant Mimosa. ...
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils. Among the genes upregulated under nitrogen limitation, we found genes involved in exopolysaccharides production and in motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly upregulated during symbiosis, we identified-besides the nif gene cluster-an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities, suggesting an important role of the cytochrome for respiration inside the nodule. The analysis of mutant strains for the RNA polymerase transcription factor RpoN (σ54) and its activator NifA indicated that-similar to the situation in α-rhizobia-P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris.
... strain TAL1145b suggests that the pyruvate obtained from the degradation of mimosine (an amino acid produced by the Leucaena leucocephala plant) can be used for glucose synthesis through gluconeogenesis (Awaya et al. 2003). Fbp is also essential for the symbiosis of the noduliferous bacteria Burkholderia phymatum STM815 with host plants (Chen et al. 2012). Expression of fructose-1,6-bisphosphatase is stimulated by the presence of ATP, such that glucose formation is favored. ...
Quantitative reverse transcription PCR (RT-qPCR) is an important tool for evaluating gene expression. However, this technique requires that specific internal normalizing genes be identified for different experimental conditions. To date, no internal normalizing genes are available for validation of data analyses for Herbaspirillum rubrisubalbicans strain HCC103, an endophyte that is part of the sugarcane consortium inoculant. This work seeks to identify and evaluate suitable reference genes for gene expression studies in HCC103 grown until middle log phase in sugarcane juice obtained from four sugarcane varieties or media with three different carbon sources. The mRNA levels of five candidate genes (rpoA, gyrA, dnaG, recA and gmK) and seven target genes involved in carbon metabolism (acnA, fbp, galE, suhB, wcaA, ORF_0127.0101 and _0127.0123) were quantified by RT-qPCR. Analysis of expression stability of these genes was carried out using geNorm and Normfinder software. The results indicated that the HCC103 dnaG and gyrA genes are the most stable and showed adequate relative expression level changes among the different sugarcane juices. The highest expression level was seen for ORF_0127.0101, which encodes a sugar transporter, in juice from sugarcane variety RB867515 and glucose as the carbon source. The suhB gene, encoding SuhB inositol monophosphatase, had a higher relative expression level on 0.5% glucose, 100% sugarcane juice from variety RB867515 and 0.5% aconitate. Together the results suggest that dnaG and gyrA genes are suitable as reference genes for RT-qPCR analysis of strain HCC103 and that juice from different sugarcane varieties modulates the expression of key genes involved in carbon metabolism.
